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comparison spades.xml @ 12:1796ea206dec draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95"
author iuc
date Thu, 16 Sep 2021 15:26:12 +0000
parents b8d633fbf5f5
children b7829778729f
comparison
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11:b8c00ce5dfa0 12:1796ea206dec
1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1">
2 <description>genome assembler for regular and single-cell projects</description> 2 <description>genome assembler for regular and single-cell projects</description>
3 <xrefs>
4 <xref type="bio.tools">spades</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <import>macros.xml</import> 7 <import>macros.xml</import>
5 </macros> 8 </macros>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">spades</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
19 </stdio> 22 </stdio>
20 <command> 23 <command>
21 <![CDATA[ 24 <![CDATA[
22 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output 25 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
23 26
24 if [[ -n \$GALAXY_MEMORY_MB ]]; then 27 if [ -n "\$GALAXY_MEMORY_MB" ]; then
25 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 )); 28 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
26 fi && 29 fi &&
27 30
28 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250} 31 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
29 #if not $kmer_choice.auto_kmer_choice: 32 #if not $kmer_choice.auto_kmer_choice: